Dear friends and colleagues, Apologies for this mass posting. Some of you have previously expressed interest in our courses for hands-on training on TADbit and TADkit (http://www.3DGenomes.org http://www.3dgenomes.org ). We are about to open a new course in the GTPB programme from the 6th to 9th of June. Additional info on the course can be found at the end of the e-mail. 3DAROC16 3C-based data analysis and 3D reconstruction of chromatin folding May we ask you to *quickly* inform us if you would be interested in attending, or recommending that your collaborators would attend? We will run the course on those dates but we need to find-out whether or not we should offer it in a later date, November 2016 for example. Best, Pedro -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt
>>>>>>
Course description 3C-based methods, such as Hi-C, produce a huge amount of raw data as pairs of DNA reads that are in close spatial proximity in the cell nucleus. Overall, those interaction matrices have been used to study how the genome folds within the nucleus, which is one of the most fascinating problems in modern biology. The rigorous analysis of those paired-reads using computational tools has been essential to fully exploit the experimental technique, and to study how the genome is folded in the space. Currently, there is a clear expansion on the wealth of data on genome structure with the availability of many datasets of Hi-C experiments down to 1Kb resolution (see for example: http://hic.umassmed.edu/welcome/welcome.php ; http://promoter.bx.psu.edu/hi-c/view.php or http://www.aidenlab.org/data.html ). In this course, participants will learn to use TADbit, a software designed and developed to manage all dimensionalities of the Hi-C data: ? 1D - Map paired-end sequences to generate Hi-C interaction matrices ? 2D - Normalize matrices and identify constitutive domains (TADs, compartments) ? 3D - Generate populations of structures which satisfy the Hi-C interaction matrices ? 4D - Analyze and compare different samples. Participants can bring- specific biological questions and/or their own 3C-based data to analyze during the course. At the end of the course, participants will be familiar with the TADbit software and will be able to fully analyze Hi-C data. Note: Although the TADbit software is central in this course, alternative software will be discussed for each part of the analysis. Target Audience The course design is oriented towards experimental researchers and bioinformaticians at the graduate and post-graduate levels. The last edition of this course was attended by people with different backgrounds and interested in the genome organization. Moreover, Hi-C data have recently been used in metagenomics studies to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. It is likely that the participants to this course aim at getting involved in generating Hi-C data for chromosome structure determination or that they just want to be able to correctly interpret and analyse publicly available data. Course Pre-requisites Recommended Linux and basic Python programming skills, graduate level in Life Sciences. Course fee Eur 360.00, lunches and coffee-breaks included. _______________________________________________ GTPB mailing list GTPB@igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb